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Major Streptomyces species associated with fissure scab of potato in South Africa including description of Streptomyces solaniscabiei sp. nov

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Abstract

Streptomyces species are the causal agents of several scab diseases on potato tubers. A new type of scab symptom, caused by Streptomyces species, was observed in South Africa from 2010 onwards. The disease was initially thought to be caused by a single Streptomyces species, however, subsequent isolations from similar symptoms on other potato tubers revealed diversity of the Streptomyces isolates. The objective of this study was to characterise these isolates in order to determine what are the major species involved in the disease. This was done by sequencing and phylogenetic analyses of the 16S rDNA as well as five housekeeping genes, investigation of growth on different culture media, standard phenotypic tests and scanning electron microscopy of culture morphology. The presence of the pathogenicity island (PAI) present in plant pathogenic Streptomyces species was also investigated. The genomes of eight isolates, selected from the three main clades identified, were sequenced and annotated to further clarify species boundaries. Three isolates of each of the three main clades were also inoculated onto susceptible potato cultivars in order to establish the pathogenicity of the species. The results of the phylogenetic and genome analyses revealed that there are three main species involved, namely, Streptomyces werraensis, Streptomyces pseudogriseolus and a novel Streptomyces species that is described here as Streptomyces solaniscabiei sp. nov., with strain FS70T (= PPPPB BD 2226T = LMG 32103T) as the type strain. The glasshouse trial results showed that all three of the Streptomyces species are capable of producing fissure scab symptoms. None of the Streptomyces isolates from fissure scab contained the full PAI and the mechanism of disease initiation still needs to be determined. Genomic comparisons also indicated that S. gancidicus Suzuki 1957 (Approved Lists 1980) is a later heterotypic synonym of S. pseudogriseolus Okami and Umezawa 1955 (Approved Lists 1980).

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Acknowledgements

Mr. Allan Hall of the laboratory for microscopy and microanalysis at the University of Pretoria is thanked for assistance with electron microscopy. Ms Kate Phetla and Mr Nthako Supu is thanked for assistance in collection of samples as well as assistance in the laboratory and glasshouse trials. We further acknowledge Potatoes South Africa (PSA) the National Research Foundation Research and Technology Fund (NRF-RTF) [UID98601] and the NRF-Technology and Human Resources in Industry Partnership (NRF-THRIP) [UID 96369] for financial assistance that made this study possible. The authors have no conflict of interest. No ethical clearance was required.

Funding

Funding was provided by Potatoes South Africa (PSA) the National Research Foundation Research and Technology Fund (NRF-RTF) [UID98601] and the NRF-Technology and Human Resources in Industry Partnership (NRF-THRIP) [UID 96369].

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Authors and Affiliations

  1. Agricultural Research Council-Vegetables, Industrial and Medicinal Plants (ARC-VIMP), Crop Protection Division, Roodeplaat, Pretoria, 0001, South Africa

    E. M. Cruywagen, K. A. Chauke, B. Z. Nkosi & M. Cloete

  2. Agricultural Research Council, Biotechnology Platform, Onderstepoort, Pretoria, 0001, South Africa

    R. E. Pierneef

  3. Department of Biotechnology and Food Technology, Tshwane University of Technology, Pretoria, 0001, South Africa

    K. A. Chauke

  4. Labeda Consulting, 137 South Duke Street, Lancaster, PA, 17602, USA

    D. P. Labeda

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  1. E. M. Cruywagen
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  2. R. E. Pierneef
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  3. K. A. Chauke
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  4. B. Z. Nkosi
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  5. D. P. Labeda
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  6. M. Cloete
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Contributions

Conceptualization: M. Cloete, Methodology: M. Cloete, E. Cruywagen, R. Pierneef, D. Labeda; Formal analysis and investigation: K. Chauke, Z. Nkosi, E. Cruywagen, R. Pierneef; Writing—original draft preparation: E. Cruywagen, K. Chauke; Writing—review and editing: M. Cloete, D. Labeda, R. Pierneef, Z. Nkosi; Funding acquisition: M. Cloete; Supervision: M. Cloete, E. Cruywagen.

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Correspondence to M. Cloete.

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All sequence data have been deposited on GenBank and the type culture of the novel species was deposited into 2 international culture collections.

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Cruywagen, E.M., Pierneef, R.E., Chauke, K.A. et al. Major Streptomyces species associated with fissure scab of potato in South Africa including description of Streptomyces solaniscabiei sp. nov. Antonie van Leeuwenhoek 114, 2033–2046 (2021). https://doi.org/10.1007/s10482-021-01659-8

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